Mass Effect: The End
by DracoWolf316
Summary: Instead of choosing a solution, Shepard comes to realize his indoctrinated state, and instead shoots himself. Now back in reality and free of indoctrination, Shepard must now activate the true Crucible to stop the Reaper threat. Story based on Indoctrination Theories. Rated T for mild language and suggested violence.


**A/N:** Wow, I was gone a long time. But I'm back, for now, and trying to make up for lost time. For my first story from my resurrection, here is my version of a new Mass Effect ending that will hopefully be one that appeases those who were betrayed at the end of the Mass Effect 3. Please, read all the way through to the end before leaving comments, and try to imagine the character as your own as you go through this. I just did it I the generic sense with a male, paragon Shepard, but if you had a renegade female Shepard, or a male Paragade Shepard, then just imagine them in the place of the character. Same thing goes for romancing. If you had someone different, just imagine them in place of the ones in this story. And without further a due, read on.

* * *

"Wake up." A voice echoed. Shepard opened his eyes, and slowly came to. He saw bright light everywhere. His body hurt all over. He climbed onto his hands and knees, then slowly began to stand. With shaky legs, he found his footing. In front of him was the glowing form of the child he'd seen before.

"What?" He groaned, holding his side. He looked around to find himself in a vast space, with a pathway leading beyond where the child stood, to glowing lights. All around this was outer space, where the battle of earth was continuing against the Reapers.

"Where am I?" He questioned. The child turned to face the giant machine behind him.

"The Citadel. It's my home." The child stated, though with an odd mixture of his and a deeper voice. Shepard faced the child.

"Who are you?" He asked. The child turned to face him again.

"I am the Catalyst." He answered. Shepard gave a confused look.

"I thought the citadel was the Catalyst." He said. The child…Catalyst pursed its lips.

"No." It answered. "The Citadel is a part of me." Shepard limped forward towards it.

"I need to stop the Reapers." He said. "Do you know how I can do that?" The Child turned away from Shepard.

"Perhaps." It answered. "I control the Reapers. They are my solution." He began walking down the path. Shepard was now more curious than before. He followed the Catalyst, limping down with him.

"The solution?" He asked. "To what?" The Catalyst seemed to stop for a moment, as if hesitating then continued.

"Chaos." It simply said. Shepard stopped at this remark. Something about its hesitation seemed off. He shook his head. _"Obviously it was caught off guard because of the time it's been here."_ He thought. He continued to follow the Catalyst.

"The created will always rebel against their creators. But we found a way to stop that from happening. A way to restore order for the next cycle." Once again, Shepard stopped.

"By wiping out organic life?" The Catalyst stopped in the center of the path.

"No, we harvest advanced civilizations, leaving the younger ones alone. Just as we left your race alive the last time we were here."

"But you killed the rest." Shepard argued.

"We helped them ascend, so they could make way for new life, storing the old life in Reaper form." Shepard looked out to the left to see a reaper floating by, attacking a Turian ship.

"I think we'd rather keep our own form." Shepard commented.

"No, you can't!" The Catalyst answered immediately, facing Shepard. It then continued in a calmer voice. "Without us to stop it, synthetics would destroy all organics." It turned away from him to look at the Reapers nearby. "We created the cycle to ensure that it never happens. That is the solution." Shepard shook his head.

"But you're taking way our future." He croaked, coughing up a little blood. "Without a future, we have no hope. With no hope, we might as well be machines; programmed to do what we're told."

"You have hope, more than you think." The Catalyst quickly answered. Shepard began to sense something was wrong with this whole situation. First, it answered late about something that it should have known right away, and when he commented on his own form, it answered too quickly.

"That fact that you are standing here, the first organic ever, proves it." The Catalyst continued. "But it also proves that my solution won't work anymore."

"So now what?" Shepard asked. the Catalyst turned to face the lights before them on the path.

"We need to find a new solution." It answered.

"Yeah, but how?" Shepard asked.

"The Crucible changed me, gave me new possibilities." The Catalyst stated. "But I can't make them happen." It turned to a section that glowed red.

"I know you've thought about destroying us." The catalyst said. "You can wipe out all synthetic life if you want." Shepard looked at the red part with great interest.

"Even you are partly synthetic. You will not survive if you choose this option." The Catalyst stated. Shepard turned towards it.

"But the Reapers will be destroyed?" He asked. The Catalyst paused for a few seconds.

"Yes." It finally answered. "But the peace won't last. Soon, your children will create synthetics, and the chaos will come back." This time, the voice of the Catalyst seemed darker in tone. Shepard noted this.

"Or, do you think you can control us?" The Catalyst continued. It looked towards a blue glowing machine, with two columns of energy. Shepard coughed a bit, coughing up a little more blood.

"So, the Illusive Man was right after all." He said.

"Yes, but he could never have taken control, because we already controlled him."

"But I can." Shepard stated.

"You will die. You will control us, but you will lose everything you have." The Catalyst stated.

"But the Reapers will obey me?" Shepard asked.

"Yes, but there is another solution." The Catalyst stated. Shepard raised an eyebrow at this.

"Synthesis." The Catalyst turned to the green energy beam ahead, between the controls and destroy options.

"And that is…?"

"Add your energy to the Crucible's. Everything you are will be absorbed, and then sent out." The Catalyst turned to face Shepard.

"The Chain reaction will combine all synthetic and organic life into a new framework; a new DNA." Shepard looked warily at this option before him.

"I…don't know."

"Why not?" The Catalyst questioned. "Synthetics are already part of you. Can you imagine your life without them?" Shepard thought on this option longest.

"And there will be peace?" He asked.

"The Cycle will end. Synthesis is the final evolution of life." The Catalyst told him. "But we need each other to make it happen." Shepard looked to the three options again.

"You have a difficult decision." The Catalyst told him. "Releasing the energy of the Crucible will end the cycle, but, it will also destroy the mass relays." It turned towards the three options.

"The paths are open, but you have to choose." With that, three platforms rose from the bottom, giving access to the three options. Shepard looked at each one.

"_Any option I choose, I die."_ Shepard thought. _"And the only one that destroys the reapers destroys all other synthetics with it." _He turned his head to the blue light.

"_If I choose to control the reapers, it would call off the attack, but the reapers would still be in existence." _ His gaze turned to the central light.

"_And if I choose to combine synthetic life and organic life, the Reapers would still be in existence as well. There's no winning option here." _He thought. He turned back to the Catalyst.

"What is this really?" He asked.

"What do you mean?" The Catalyst asked. "These are your only options."

"No, I mean what is this place? This was not in the final plans of the Crucible. This place cannot exist." He stated. The Catalyst looked around, then back at him.

"No, this does exist. You must choose a path for the-"

"Why are each stations colored like this?" He said, pointing to the three different stations. "What is the point of those lights?! And why aren't there any mass shields around this area?! We're exposed to direct space!" The Catalyst backed up a little, fear now appearing on its face.

"And another thing." Shepard said.

"How will controlling the Reapers solve anything?! I would become just as they are and be controlling everything! That still has the Reapers in direct power. If I bonded all organic life with synthetic life, how is that any different from those husks that the Reapers create?! And destroying all synthetic life? That's just another way of proving your point that synthetics and organics cannot coexist!"

Shepard pointed out into the battle. "Have you even seen the Geth and the Quarians fighting out there, side by side!? Or perhaps the fact that on my ship, an organic and synthetic have started to romance each other?!" Shepard then turned around to where he came from.

And what about back there, at the control pad? How did Anderson make it to the control pad before I did? Admiral Hackett clearly stated no made it on board. Heck, how did he even know I was on board when he contacted me?!"

"This is irrelevant!" The Catalyst shouted.

"You're scared now, aren't you?" Shepard asked. "You know I'm getting closer to the truth."

"You are at the truth Shepard!" The Catalyst insisted. "This is what you want."

"No. What I want is the destruction of the Reapers, and the survival of the synthetic races outside of them. This is what the Crucible was designed to do. It was not made to be controlled like this. This place isn't what anyone wanted at all." Shepard's mind clicked.

"That's it, isn't it? This place can't exist, because it doesn't exist, am I right?" The Catalyst grew eerily calm.

"I never made it onto the station. I'm still down on earth, aren't I?" He points to the catalyst.

"You're not even real, and the boy you appear as never existed either, did he? This entire time, I've been indoctrinated myself." He looked to his pistol.

"What are you doing?" The Catalyst asked.

"Like I said to The Illusive Man, I'd rather die than see myself indoctrinated." He raised the pistol to his chin.

"Stop!" The Catalyst shouted.

"I will not be controlled." Shepard said. He pulled the trigger.

* * *

"Shepard! Get a move on!" Garrus's voice shouted at him. Shepard rolled on the ground just as another laser almost clipped him. He stood and began running towards the beacon, only now, it looked more in sync with reality than before. Beside him were Garrus and Liara, charging towards the beacon with great haste. Harbinger above them was now growling very loud and angrily, as it continued firing it's lasers down at them. Suddenly, one was headed right for them! Shepard went to dodge, but it wasn't enough! Suddenly, he felt himself being pushed. He turned his head to see Liara pushing him further away from the laser with her biotics, while also using gravity well to pull herself and Garrus out of the way as well.

"Shepard! We will distract Harbinger. You must make it to the Crucible!" Garrus shouted to him.

"Go! Now!" Liara shouted. Shepard didn't have time to argue. More lasers were being fired down. Shepard sprinted faster than he ever had to before, almost at the beacon. One final laser began to come down. It was the largest one yet. Shepard had no time to think about this. He ran straight at the beacon, and jumped. There was a bright light.

* * *

Shepard found himself in a large circular area, surrounded by a sphere. All around him, there were just gray walls. He saw a single pedestal nearby. He walked to it. A single light glowed in the center of it. He pressed it. Suddenly, the entire interior of the sphere lit up, and a large hologram of the galaxy appeared. On it was the pinpointed locations of every mass relay, every reaper, the Citadel, and anything that appeared to be controlled by them. A voice suddenly appeared.

"This was our hope. That one day, a member of the galaxy would be able to unite the whole, and stop the chaos that ripped it apart era after era. You are now at the seat of power for the crucible. You alone have the power to eliminate the threat of the Reapers, where we had failed." A single button appeared on the pedestal, below the gigantic holo map above it.

"You must destroy the Reapers. End the suffering of a million species that now reside in those hollow shells of machinery. End the suffering of the entire galaxy. End what we never could." Shepard looked down at the button. The white light offered no sign of betrayal, or any deviation from his own goals. This was indeed the true form of the crucible. Shepard reached out.

"I don't think so Commander." A voice said behind him. Commander Shepard turned to see The Illusive Man staring him down, with a pistol aimed for his head.

"That power will be mine and mine alone."

"Didn't you just hear the message?" Shepard said. "There's no way to control the Reapers! You can't win this." He said.

"That's where you're wrong commander." The Illusive Man said. "I can still control them. But I can't do it if you push that button. We can still save humanity."

"Listen to yourself!" Shepard shouted. "I'm this close to actually stopping the Reapers and sparing the lives of millions of people, humans included, and you're still trying to let the Reapers gain control!"

"NO!" TIM shouted. "I am in control. I have the power to control the reapers! I will control everything!"

"Then how can you do it without letting the reapers take humanity away?" Shepard asked. "How will you control them in the next few hours?"

TIM seemed to hesitate at this.

"I…I'll save humanity. I can control the reapers-"

"HOW!" Shepard shouted. "They've already indoctrinated you. Heck, I was almost indoctrinated myself! They're in your mind, trying to steer you in the direction that leads to their preservation. Their existence." He looked TIM straight in the eye.

"If you know what's good for humanity, you know what needs to be done." He said. The Illusive Man began to struggle a bit. He raised the pistol up higher, and staggeringly, pointed it to his forehead.

"I'm sorry…Please…Forgive me…"He fired. He fell to the edge of the platform, before falling off into the bottom of the sphere. Shepard tipped his head to where The Illusive Man once stood, before turning around and pressing the button.

"It is done." The voice said. "The crucible will activate in 1 minute. Evacuate now." Shepard saw a bright light begin to form around the edges of the crucible's walls. A massive amount of energy was gathering.

"Shit!" Shepard shouted. He turned around, and saw that a mass-relay had appeared from the floor. He quickly ran towards it, and jumped through.

* * *

The Normandy was flying around the Citadel, weaving in and out of other ships as they fired continuously at the reapers.

"Something is happening with the Crucible!" Admiral Hackett's voice penetrated the radio channels of each ship.

"All ships, prepare for evacuation to the rondevu site."

"Jeff!" EDI shouted to him from her console.

"EDI, I'm not leaving the Commander behind!" Joker said to her.

"I know. I was going to remind you of that." EDI said. Joker gave a little smirk and continued to hold his course to the crucible.

* * *

Commander Shepard found himself on the presidium, at the council chamber. He activated his communicator.

"Joker! I'm on the Presidium in the council Chambers! I need an immediate evac!"

"Commander? Boy it's glad to hear your voice. The Normandy is nearly there; we need you at the nearest airlock." Joker informed him.

"There' no time. The crucible will be active in 50 seconds!" Commander Shepard shouted.

"We can make it Commander! We'll get you out of there!" Joker said.

"Joker, you and I both know you won't get here in time. Go to the evac site. Leave me, that's an order!"

"Commander, we won't leave you!" Joker said. EDI though knew the chances of Commander Shepard making it out of there as well. She placed her hand on Jeff's shoulder.

"Jeff. Let it go. If we don't make it out of here, then we could die as well." She said.

"But…the Commander." Joker said. He looked into her eyes, and saw how much it pained her as well. Joker squeezed his eyes shut and turned back to the console.

"It's been an honor Commander." Joker said.

"Go, now!" Commander shouted. Joker turned the ship around and began weaving his way back out of the Reapers and ships before entering FTL travel with the rest of the evacuees.

* * *

Commander Shepard looked around the Presidium, and felt the station begin to rumble. Outside, he saw the explosion clouds emanating from the outstretched arms of the Citadel, as the Crucible began to glow a bright white. Energy storms began to surge around him. He looked for anything that could be used to escape. Suddenly, he noticed something: a stealth-class Alliance ship stuck in a wall nearby, still burning from a crash landing into the Citadel, right on the other side of the Presidium. He made a run for it.

_"There may still be escape pods in it." _ he thought. He arrived, with forty seconds to spare. Wasting no time, he took out his pistol and fired several shots at the view-plate, cracking it. He jumped onto the hull, and smashed through the broken screen, tumbling inside. Thirty seconds! He jumped up, and made a dash for the back of the ship. There was a set of doors ahead, one malfunctioning with a constant opening. Shepard timed himself, swiftly passing it just before it closed back down on the other door. there were now only twenty estimated seconds before the firing of the Crucible!. He took a quick look around the room, and there on the right and left walls were escape pods. He jumped over a burning body that was unfortunate to be caught in the crash as he made his way to a pod in the back. Pressing the activation button, he ran inside the pod as soon as it opened. The time was running short. By his mind, he had about 15 seconds left. The air-lock sealed, and he pressed the escape button inside. The pod hissed before launching him into outer space, around Earth's orbit.

* * *

5…

4…

3…

2…

1…

The Crucible sent an energy pulse out from its epicenter, a wave of white light washing over everything. The Reapers who were caught up in it immediately jerked about before halting in moving; now just floating in space.

On earth, the husks began dropping in masses, becoming nothing but lifeless bodies once more. The Reapers there immediately began to fall, crashing into the ground. Soldiers everywhere were cheering in response to this. Near the beacon, Liara and Garrus stood silently, watching as the waves emanated from the Citadel in orbit, before the citadel itself began to be consumed in a fireball.

* * *

The Charon Mass Relay at the end of the solar system was rotating at its constant pace, before the wave of white light hit it. Suddenly the stabilizing rings stopped, and began rotating in the opposite direction at a rapid pace before locking in place and shooting a white beam out into space, self-destructing in the process. The waves of light began traveling to all Mass relays in the entire Galaxy, completely shutting them down as the Reapers continued to be exterminated from the Galaxy.

* * *

A lone blue streak turned to red, then yellow, then white as it entered earth's atmosphere. The pod began to accelerate towards an area in northern Europe. Finally, it made impact in the red sea. A few moments later, a single person floated to the surface, bruised, cut and bleeding, but alive. He looked out at the Reapers as they continued to shut down. As he did, he activated his comm.

"Garrus, Liara?" Shepard called out. There were a few moments of silence.

"Shepard?!" Liara shouted. "Is it really you?!"

"Yes, it's me. I'm alive." He said.

"Son of a bitch. Nothing can keep you down." Garrus entered.

"Are you both okay?" Shepard asked.

"Yes, Shepard. We're okay. I think, everything will be okay now."

* * *

It took sometime before contact was established again with the evac ships. Everyone had made it safe and sound to the evac site. Fortunately, the Crucible didn't drain the power like was previously thought, and all synthetic life was still active and about. After communication had been established, the plans to reconstruct the Mass relays were founded. With help from data collected from the Conduit, within the next decade, a working Mass relay was constructed to the Evac Site, where another one was created within another six years with the help of the Quarians and Geth. Creating Mass Relays in the other systems would take some time, but with the two created, many were finally able to return to their home systems as war heroes and heroines.

In the Serpent Nebula, construction on a new Citadel had already begun. Many races were coming together for the first time to help rebuild the galaxy, and though it would take some time, the new things being learned between races would only serve to strengthen their bonds in the projects.

Relations between many races were now being built and rebuilt. The Quarian people, not having not only fought alongside the Geth, but now rebuilding with them, have come to see just what they have created, and have finally accepted the geth as an individual race. The return to their home world would allow for them to start regaining the immunity that had been stripped from them in the 3 centuries on the flotilla.

Meanwhile, the Geth; now with the addition of individuality amongst themselves, have decided to forgo their decision to reformat into a giant collective, and instead have decided to become a part of the galactic community. While there were still suspicions, after a century of living amongst them, they have become widely accepted by many races.

The Krogan, now freed from the genophage that plagued their population for so long, have started to reproduce again, only this time they were taking it slower than before, not wishing another threat like the genophage again. Under the leadership of Urdnot Wrex, their home world was reformed, and their culture once again began to flourish.

After the actions that had been shown by the last Council, a new one had been formed, this time of members from each of the citadel races, and it had been decided upon that a new member would be elected from each race every ten years. This council now consisted of members from the Asari, Turian, Salarian, and Human races, as well as newly added members from the Hanar, Volus, Quarian, Krogan, Geth, and Drell.

As for the fallen comrades lost in battle, their names were forever inscribed on a memorial found on every home-world's capital, for the names of each brave soldier that had been lost in the fight. The list included some members of the Normandy, who gave their lives to see the future of the other races.

For the living members, Tali and Garrus continued their relationship after fifteen years apart, and settled on Rannoch. Joker and EDI continue to pilot the Normandy, but have been in a constant relationship on the side ever since the end of the war. Javik began working with several historians, including Liara, to teach them about the culture and ways of the Protheans. Kaidan/Ashley continued in their service to the Alliance, still onboard the Normandy alongside Joker, EDI and James. As for Commander Shepard, after a long and exhausting period of service, immediately retired after receiving honors and recognition for his/her leadership and actions during the Reaper war. He/she settled down with Liara on the Shadow Broker's Ship, occasionally meeting up with their comrades and friends every so often to reminisce about their lives and catch up.

* * *

"And that's the story of the greatest hero of the galaxy little one."

"Please, can you tell me another story about you grandpa, Grandpa?"

"Ha-ha, you are curious, aren't you little one?" He asked. "Alright. This one isn't as interesting, but it certainly is quite the tale."

* * *

And that my good people of FanFiction, is my ending for the Mass Effect Universe. This kind of ending would be if there was a reworking of the War Assets to allow this as the ending at 5,000 points. For the people who had different romance options or different actions, try to imagine the outcome in your version. I just did it in the generic version that was set out since the beginning. If you have any questions or comments, or even ways to improve this story, please leave your review and I'll fix what I can (No Flames allowed.)


End file.
